The Census of 1860 showed some major changes to the family composition. John Thompson, age 26, was listed as head of household. That matches John W., who had been age 16 when the 1850 Census was taken. John's siblings from earlier Census, James K., Araminta, Nancy, and Leander were shown still in the household. Two new names, John T. Thompson, age 11 and James Johnson, age 5, could be siblings born since the 1850 Census but the family already had members with names John and James.

After surviving the fighting at Antietam (Sharpsburg), often called the bloodiest day of the Civil War, Pvt. John W. Thompson, was killed in fighting at Marye's Heights, Fredericksburg, on December 13, 1862. The fighting continued there through December 15.